Thank you. Someone had already suggested TarBase. Maybe you did. Since these files are often changed ... at least they should be .... we would like to implement a procedure that download such files and process them as automatically as possible. TarBase provides a download file which is actually an XLS file compressed as a rar archive. I found the R function to download the file. But I could not find any R function capable of uncompressing rar-archives. There are function for uncompressing Z and gz archives that I tried out. They do not seem to understand the rar format, as expected. Maybe the only way is to uncpmplress such rar file through a system command ? Regards, Maura -----Messaggio originale----- Da: michael watson (IAH-C) [mailto:michael.watson@bbsrc.ac.uk] Inviato: sab 01/05/2010 11.29 A: mauede@alice.it; Bioconductor List Oggetto: RE: [BioC] Validated miRNAs revisited Tarbase and miRecords are the only databases of validated targets I know of. MirWalk has a validated section but I think it comes from text mining. ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of mauede@alice.it [mauede@alice.it] Sent: 01 May 2010 06:11 To: Bioconductor List Subject: [BioC] Validated miRNAs revisited I apologize for asking again the same question I asked some months ago. The reason is that a question has been raised recently by people I work with. The question stemmed from the double meaning of the word "validated" with reference to miRNAs. Some time ago I downloaded the Fasta files "mature.fa" and "matureStart.fa" (the latter cannot be found any more). I meant to get miRNAs that have been experimentally validated against (binding to) some gene targets. I used the dat set "hsTargets" avaiilable with Bioconductor to find the matching miRNA-terget pairs. The question arisen is: "are the nmiRNAs I got just predicted by some code (miRanda or the like) or have they been experimentally validated" ? I would appreciate your comments. Thank you in advance Maura tutti i telefonini TIM! [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor tutti i telefonini TIM! [[alternative HTML version deleted]]

On Mon, May 3, 2010 at 9:03 AM, <mauede@alice.it> wrote: > Thank you. > Someone had already suggested TarBase. Maybe you did. > Since these files are often changed ... at least they should be .... we > would like to implement a procedure that > download such files and process them as automatically as possible. > TarBase provides a download file which is actually an XLS file compressed > as a rar archive. > I found the R function to download the file. But I could not find any R > function capable of uncompressing rar-archives. > There are function for uncompressing Z and gz archives that I tried out. > They do not seem to understand the > rar format, as expected. > Maybe the only way is to uncpmplress such rar file through a system command > ? > > Hi, Maura. It looks like this file has not been updated since 2008, so I doubt that you will need to perform this operation very often. Yes, a system() call would be one way to go for extracting from a rar file. Sean > > -----Messaggio originale----- > Da: michael watson (IAH-C) [mailto:michael.watson@bbsrc.ac.uk] > Inviato: sab 01/05/2010 11.29 > A: mauede@alice.it; Bioconductor List > Oggetto: RE: [BioC] Validated miRNAs revisited > > Tarbase and miRecords are the only databases of validated targets I know > of. MirWalk has a validated section but I think it comes from text mining. > ________________________________________ > From: bioconductor-bounces@stat.math.ethz.ch [ > bioconductor-bounces@stat.math.ethz.ch] On Behalf Of mauede@alice.it [ > mauede@alice.it] > Sent: 01 May 2010 06:11 > To: Bioconductor List > Subject: [BioC] Validated miRNAs revisited > > I apologize for asking again the same question I asked some months ago. > The reason is that a question has been raised recently by people I work > with. > The question stemmed from the double meaning of the word "validated" with > reference to miRNAs. > Some time ago I downloaded the Fasta files "mature.fa" and "matureStart.fa" > (the latter cannot be > found any more). > I meant to get miRNAs that have been experimentally validated against > (binding to) some gene targets. > I used the dat set "hsTargets" avaiilable with Bioconductor to find the > matching miRNA-terget pairs. > > The question arisen is: "are the nmiRNAs I got just predicted by some code > (miRanda or the like) or have they been experimentally validated" ? > > I would appreciate your comments. > > Thank you in advance > Maura > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

There's a couple of things of note here. Last time I looked, TarBase had about 1300 records and miRecords 1600. This data covers a number of species, across hundreds of microRNAs and 10000's of genes per species. The take home message is that these databases are hopelessly incomplete, and cover only a fraction of miRNA:gene interactions. This is not a criticism of either, but often in whole genome assays, one needs more coverage than these two provide. The second thing I'd say is to look carefully at the evidence code. For instance, in TarBase, for mir-155, about 100 of the records come from a single paper, which used pSILAC as their method. Now, I encourage you to read the paper, but to summarise, pSILAC is a proteomics based method; the authors essentially altered the expression of specific microRNAs and then looked at which PROTEINS differed subsequently. Of course, microRNAs do not act on proteins directly (as far as we know), they act on messenger RNA. So these proteomic effects, as far as I can tell, could be primary (e.g. the miRNA suppresses the mRNA and therefore no protein gets made) or secondary (e.g. the miRNA suppresses the mRNA of a transcription factor and therefore less targets of the transcription factor are made). I guess what I am trying to say is that there are different definitions of "validated" targets, and these databases may contains genes which are not directly targetted by microRNAs, but which form parts of systems that are targetted by them Mick ________________________________________ From: mauede@alice.it [mauede@alice.it] Sent: 03 May 2010 14:03 To: michael watson (IAH-C); Bioconductor List Subject: R: [BioC] Validated miRNAs revisited Thank you. Someone had already suggested TarBase. Maybe you did. Since these files are often changed ... at least they should be .... we would like to implement a procedure that download such files and process them as automatically as possible. TarBase provides a download file which is actually an XLS file compressed as a rar archive. I found the R function to download the file. But I could not find any R function capable of uncompressing rar-archives. There are function for uncompressing Z and gz archives that I tried out. They do not seem to understand the rar format, as expected. Maybe the only way is to uncpmplress such rar file through a system command ? Regards, Maura -----Messaggio originale----- Da: michael watson (IAH-C) [mailto:michael.watson at bbsrc.ac.uk] Inviato: sab 01/05/2010 11.29 A: mauede at alice.it; Bioconductor List Oggetto: RE: [BioC] Validated miRNAs revisited Tarbase and miRecords are the only databases of validated targets I know of. MirWalk has a validated section but I think it comes from text mining. ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of mauede@alice.it [mauede@alice.it] Sent: 01 May 2010 06:11 To: Bioconductor List Subject: [BioC] Validated miRNAs revisited I apologize for asking again the same question I asked some months ago. The reason is that a question has been raised recently by people I work with. The question stemmed from the double meaning of the word "validated" with reference to miRNAs. Some time ago I downloaded the Fasta files "mature.fa" and "matureStart.fa" (the latter cannot be found any more). I meant to get miRNAs that have been experimentally validated against (binding to) some gene targets. I used the dat set "hsTargets" avaiilable with Bioconductor to find the matching miRNA-terget pairs. The question arisen is: "are the nmiRNAs I got just predicted by some code (miRanda or the like) or have they been experimentally validated" ? I would appreciate your comments. Thank you in advance Maura tutti i telefonini TIM! [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM! Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer